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    Pcdh9 protocadherin 9 [ Mus musculus (house mouse) ]

    Gene ID: 211712, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Pcdh9provided by MGI
    Official Full Name
    protocadherin 9provided by MGI
    Primary source
    MGI:MGI:1306801
    See related
    Ensembl:ENSMUSG00000055421 AllianceGenome:MGI:1306801
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
    Expression
    Biased expression in cerebellum adult (RPKM 14.4), cortex adult (RPKM 12.5) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pcdh9 in Genome Data Viewer
    Location:
    14 E2.1; 14 45.8 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (93251136..94132619, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (93013700..93892834, complement)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_37386 Neighboring gene STARR-seq mESC enhancer starr_37387 Neighboring gene predicted gene, 24127 Neighboring gene heat shock protein 8 pseudogene Neighboring gene STARR-seq mESC enhancer starr_37389 Neighboring gene STARR-seq mESC enhancer starr_37390 Neighboring gene STARR-seq mESC enhancer starr_37392 Neighboring gene STARR-seq mESC enhancer starr_37394 Neighboring gene predicted gene, 23509 Neighboring gene nucleophosmin 1 pseudogene Neighboring gene L-lactate dehydrogenase A pseudogene Neighboring gene STARR-seq mESC enhancer starr_37395 Neighboring gene STARR-seq mESC enhancer starr_37396 Neighboring gene predicted gene, 23324 Neighboring gene predicted gene, 18074

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Deficiency of protocadherin 9 leads to reduction in positive emotional behaviour. Uemura M, et al. Sci Rep, 2022 Jul 13. PMID 35831353, Free PMC Article
    2. Cadherin expression in the somatosensory cortex: evidence for a combinatorial molecular code at the single-cell level. Krishna-K K, et al. Neuroscience, 2011 Feb 23. PMID 21129452
    3. Genetic Mapping in Mice Reveals the Involvement of Pcdh9 in Long-Term Social and Object Recognition and Sensorimotor Development. Bruining H, et al. Biol Psychiatry, 2015 Oct 1. PMID 25802080
    4. Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14. Strehl S, et al. Genomics, 1998 Oct 1. PMID 9787079
    5. Single-Cell Transcriptomics Reveals Regulators of Neuronal Migration and Maturation During Brain Development. Pensold D, et al. J Exp Neurosci, 2018. PMID 29551912, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deficiency of protocadherin 9 leads to reduction in positive emotional behaviour.
      Title: Deficiency of protocadherin 9 leads to reduction in positive emotional behaviour.
    2. Quantitative analysis of basic mouse behavior uncovered a role for Pcdh9 in specific cognitive functions required for long-term recognition, involvement of Pcdh9 in sensory cortex development and showed effect of its deletion on sensorimotor behaviors
      Title: Genetic Mapping in Mice Reveals the Involvement of Pcdh9 in Long-Term Social and Object Recognition and Sensorimotor Development.
    3. The results of this study demonistrated that the distribution of Pcdh9 protein in the olfactory bulb, retina, spinal cord, and dorsal root ganglion
      Title: Distribution of protocadherin 9 protein in the developing mouse nervous system.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (3)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cell-cell contact zone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in growth cone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protocadherin-9

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001081377.3 → NP_001074846.1  protocadherin-9 isoform a precursor

      See identical proteins and their annotated locations for NP_001074846.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a, also known as 3).
      Source sequence(s)
      AC122355, AC123919, AC125095, AC132470, CF745283
      Consensus CDS
      CCDS36992.1
      UniProtKB/TrEMBL
      B2RY69, F8VPK8
      Related
      ENSMUSP00000141396.2, ENSMUST00000195826.6
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    2. NM_001271798.1 → NP_001258727.1  protocadherin-9 isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an in-frame exon, compared to variant 1. The encoded isoform (b, also known as 2) is shorter than isoform a.
      Source sequence(s)
      AC123919, AC125095, AC132470
      Consensus CDS
      CCDS79350.1
      UniProtKB/TrEMBL
      A0A0A6YWY8, B2RY66
      Related
      ENSMUSP00000141759.2, ENSMUST00000193901.6
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    3. NM_001271799.1 → NP_001258728.1  protocadherin-9 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains multiple differences in the 5' UTR and coding region, compared to variant 1. It initiates translation at an alternate start codon. The encoded isoform (c) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC123919, BC060736, CJ107832
      Consensus CDS
      CCDS79352.1
      UniProtKB/TrEMBL
      A0A0A6YY37, B2RXR7
      Related
      ENSMUSP00000142260.2, ENSMUST00000192221.6
      Conserved Domains (2) summary
      cd11304
      Location:453 → 548
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:654 → 874
      Protocadherin; Protocadherin

    4. NM_001271800.2 → NP_001258729.1  protocadherin-9 isoform d precursor

      See identical proteins and their annotated locations for NP_001258729.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame exon and uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (d, also known as 4) is shorter than isoform a.
      Source sequence(s)
      AC123919, AC125095, AC132470, CF745283
      UniProtKB/TrEMBL
      B2RXR7
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    5. NM_001346722.1 → NP_001333651.1  protocadherin-9 isoform e precursor

      Status: REVIEWED

      Source sequence(s)
      AC122355, AC123919, AC125095, AC132470
      Consensus CDS
      CCDS84156.1
      UniProtKB/TrEMBL
      A0A0A6YY09, B2RXR7
      Related
      ENSMUSP00000142224.2, ENSMUST00000195376.6

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000080.7 Reference GRCm39 C57BL/6J

      Range
      93251136..94132619 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006518777.5 → XP_006518840.1  protocadherin-9 isoform X2

      UniProtKB/TrEMBL
      B2RXR7
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin

    2. XM_036158532.1 → XP_036014425.1  protocadherin-9 isoform X1

      UniProtKB/TrEMBL
      B2RY69
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin

    RNA

    1. XR_003950833.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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